20-37776514-A-G

Position:

• chr20-37776514-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030877.5(CTNNBL1):​c.751-831A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,052 control chromosomes in the GnomAD database, including 34,775 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (34775 hom., cov: 32)
• Consequence: CTNNBL1 NM_030877.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

Genes affected

CTNNBL1 (HGNC:15879): (catenin beta like 1) The protein encoded by this gene is a component of the pre-mRNA-processing factor 19-cell division cycle 5-like (PRP19-CDC5L) protein complex, which activates pre-mRNA splicing and is an integral part of the spliceosome. The encoded protein is also a nuclear localization sequence binding protein, and binds to activation-induced deaminase and is important for antibody diversification. This gene may also be associated with the development of obesity. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been defined on the X chromosome. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNBL1	NM_030877.5	c.751-831A>G		intron_variant		ENST00000361383.11	NP_110517.2
CTNNBL1	NM_001281495.2	c.670-831A>G		intron_variant			NP_001268424.1
CTNNBL1	XM_024451947.2	c.670-831A>G		intron_variant			XP_024307715.1
CTNNBL1	XM_011528917.3	c.421-831A>G		intron_variant			XP_011527219.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTNNBL1	ENST00000361383.11	c.751-831A>G		intron_variant		1	NM_030877.5	ENSP00000355050.6
CTNNBL1	ENST00000628103.2	c.670-831A>G		intron_variant		2		ENSP00000487198.1

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102618 AN: 151934 Hom.: 34747 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.707

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.675 AC: 102696 AN: 152052 Hom.: 34775 Cov.: 32 AF XY: 0.677 AC XY: 50305 AN XY: 74318

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.710

Alfa AF: 0.683 Hom.: 46673

Bravo AF: 0.674

Asia WGS AF: 0.801 AC: 2784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.26

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs238302; hg19: chr20-36404916;